GENERATION OF SUB-WAVELENGTH ACOUSTIC STATIONARY WAVES IN MICROFLUIDIC PLATFORMS: THEORY AND APPLICATIONS TO THE CONTROL OF MICRO-NANOPARTICLES AND BIOLOGICAL ENTITIES. A Dissertation Presented to the Faculty of the Graduate School of Cornell University in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy by Muhammet Kursad Araz February 2010 c 2010 Muhammet Kursad Araz ALL RIGHTS RESERVED GENERATION OF SUB-WAVELENGTH ACOUSTIC STATIONARY WAVES IN MICROFLUIDIC PLATFORMS: THEORY AND APPLICATIONS TO THE CONTROL OF MICRO-NANOPARTICLES AND BIOLOGICAL ENTITIES. Muhammet Kursad Araz, Ph.D. Cornell University 2010 Presented in this dissertation are the theoretical modeling and experimental re- sults of a novel method for manipulating micro and nanoparticles in an acoustically actuated microfluidic glass capillary. Here, the PZT (Lead Zirconate Titanate)- glass capillary actuator mechanism performs bioanalytical methods such as collec- tion, separation and mixing at microscale, at low voltage drives, enabling produc- tion of battery operated inexpensive portable microfluidic systems. Analytical and finite element modeling of the vibrational modes of the fluid filled thick walled cylindrical capillary has been also studied. Torsional, longitudi- nal and flexural modes and their dispersion relationships are presented. Through the excitation of the various vibrational modes of the silica capil- lary, sub-wavelength acoustic pressure modes in the microfluidic cavity are formed. More than 20 such sub-harmonic modes are generated harmonically in the 20kHz- 2MHz regime whereas naturally occurring radial modes have a cut off frequency around 9 MHz. The amplitude of these stationary acoustic pressure fields are high enough to generate nonlinear acoustic forces and streaming effects for micro and nanoparticle manipulation. Theoretical models explaining the generation of the sub-wavelength modes and acoustic radiation forces are developed. Generation of an effective macroscopic electric field as a result of the collection of charged colloidal particles under acoustic forces has been observed. This self generated field causes fast collective diffusion of nanoparticles and can counter- balance the acoustic radiation forces, so a method for calibrating acoustic force field with respect to the collective electrostatic repulsion and the Zeta potential of particles is introduced. A silicon bulk microfabricated actuator enabling different bioanalytical capa- bilities such as collection, separation and mixing of analytes on a single bulk-PZT- silicon microfluidic platform at low voltage drives is also demonstrated. Presented experimental results include: collection of micro and nanoparticles, colloidal systems and biological entities such as bacteria and cells; separation of micro and nanoparticles with respect to acoustic contrast factor; planar chipscale centrifugation of blood; separation of microparticles with respect to size; and con- trolled oscillating bubble dynamics at the microscale, which are all obtained in the PZT-glass capillary actuator driven with a typical function generator at around 100 milliwatts of power consumption. BIOGRAPHICAL SKETCH Muhammet Kursad Araz received his B.S. degree in physics in 2001 from Bogazici University in Istanbul, Turkey and continued his graduate studies at the School of Applied and Engineering Physics Department at Cornell University. He received his Ph.D. degree in applied physics in 2009 with a minor in electrical engineer- ing. During his Ph.D. studies, he focused on the theoretical modeling and ap- plications of chipcscale novel acoustical methods for microfluidic control of micro and nanoparticles, and biological samples. His current and future research inter- ests include acoustics, MEMS and microfluidics along with their applications in bioengineering, colloidal system characterization and renewable energy harvesting methods. iii To my parents, Rifat and Gulser Araz, and my wife Yasemin iv ACKNOWLEDGEMENTS During the preparation of this study, I got tremendous help from many people. While I may have missed a few due to my memory and the rush of the approaching deadline, I will really try my best to acknowledge everyone. First of all, I would like to thank my thesis advisor, Prof. Amit Lal, for his endless trust, guidance and motivation during the course of this study. His curiosity and interest over many different scientific and engineering disciplines made this work very exciting. His wise and positive attitude in even the most awkward moments motivated me to become a more positive and more patient individual compared to what I was before. I cannot remember a single meeting with him after which I left his room without feeling energized. I also learned a lot from him about getting more professional in terms of my academic writing skills. His great motivation for providing enough resources for the development of his students is something I will remember if I have chance to be a faculty member someday. I would like to also thank Garima Goel Lal; with Prof. Lal, they always shared the warmth of their home environment and made me feel like a member of the family. I would like to also thank my committee members Prof. Clifford Pollock and Prof. Michal Lipson for their, support, feedback and input throughout this study. Furthermore, I thank Prof. David Muller and Prof. Warren Zipfel for attending to my oral exams and providing constructive feedback. I also thank Prof. Sunil Bhave for the many fruitful discussions we had. It was very exciting and informative to be the teaching assistant of the MEMS class under his supervision. I would like to thank my undergraduate advisors from Bogazici University: First Prof. Fahrunisa Neyzi for guiding me to do the right thing for myself, choosing physics as my undergraduate major; and to Prof. Levent Kurnaz with whom I started to get the real joy of doing scientific research. His easy way to approach v even very complex systems and starting all problems with the “assume a spherical horse” analogy helped me a lot not only in the course of this study but also throughout my life. I would like to also thank him for guiding me to apply for the Ph.D. program in Applied Physics Department at Cornell University, where I had really have found the study in which I am most interested. I also would like to thank my group mates, SonicMEMS’ers: Serhan Ardanuc, Alper Bozkurt, Steven Tin, Norimasa Yoshimizu, Abhishek Ramkumar, Janet Shen, Siva Prasad, Hengky Chandrahalim, Kwame Amponsah, Yue Shi, Larry Lu, Manoj Pandey and former group members Chung-Hoon Lee, Xi Chen, Shankar Radhakrishnan, Rajesh Duggirala, Il-Seok Son, Abhijit Sathaye, Shi-Herng Kan, Ville Kaajakari and Hang Guo. Over the individual encounters or group meetings, I learned many new and exciting things from all of them. Special thanks go to Hoon for guiding me in the beginning of my research, and Xi for helping me during the design of the microfabrication steps and introducing the clean room environment. A special thanks also go to my dear friend Serhan, for our very fruitful discussions over acoustic problems, and other scientific, social and political matters and also for letting me know of Prof. Lal’s moving to Cornell. I also thank Aaditya Khimani and staff members of Cornell Nanofabrication Facility and Cornell Nanobiotechnology Center for their help during the design and the fabrication of the silicon bulk actuator presented in the latter part of this thesis. I would like to thank Scott Coldren, Kelli Hulslander, Susan Ferrara, Lisa Gould, Daniel Richter, William Bader, Carmen Blankinship, and all ISSO staff members, especially Sarah Hilsman and Elizabeth Shedd, for their help related to administrative matters. I would also like to thank my editor in the beginning and new friend at the end, Jill Marie, for editing my thesis and her strong passion over vi improving my writing skills. I learned a lot from her and hope to learn more. A Turkish proverb says “Tell me about your friends, I will tell who you are.” I am not sure this would be true for me as I had really wonderful friends. I would like to thank my friends in Ithaca and elsewhere: Serhan Ardanuc, Alper Bozkurt, Hazer Inaltekin, Helena Silva, Engin Burgaz, Gokhan Arikan, Zeki Durak, Onur Tokel, Ekrem Cakmak, Omer Ilday, Ozhan Ozatay, Mahmut Aksit, Shaffique Adam, James van Howe, Abdurrahman Gumus, Arman Ajmuhanov, Abdullah Ozer, Ankush Gupta, Yildiray Yildirim, Mandy Esch, Murat Baday, Kadir Yavuz, Esref Dogan, Mehmet Sen, Askin Kocabas, Volkan Bilgili, Nuri Gokcek, Yasin Senbabaoglu, Jessie Childs and Oguzhan Vicil: and also my elder friends in Ithaca, Hatice Brenton, Mahbud and Henrike Burton, Fahri and Asu Unsal and Musaddak Ghaffur. I would like to specially thank my dear friend Ali Gokirmak and his parents Nevin and Hikmet Gokirmak for their welcoming support in my first year in Ithaca. I cannot forget the nice memories we had in their place in Maple Hill. And my family; I do not know how to thank my parents Rifat and Gulser Araz, for everything they have provided for me and their trust in me. From them I learned the importance of social values such as sharing and caring for others. I would say most of my values are shaped positively by them. One of the earliest science discussions that I cannot forget is the one that my father told me at the age of 5, about the existence of a tremendously dynamic world of moving, rotating, oscillating atoms and molecules which we cannot see at all. That discussion still stays as the seed source of my enthusiasm over scientific research. I would like to say that his reflective attitude over nature spanning a broad range from stars in the sky to the cells in our stomach and strong belief in the importance of good education as a life long investment shaped my career interests. From him first, I learned if something exists, there is a purpose for it. I also would like to thank vii my siblings Gulsum and Kadir Araz for their support and affection for me.